Arrangement of the Sense and Stop Codons of the Template in the A Site of the Human Ribosome as Inferred from Crosslinking with Oligonucleotide Derivatives

• Published in: Molecular biology (New York) 2003-11, Vol.37 (6), p.866-873
• Main Authors: Styazhkina, V. A., Molotkov, M. V., Demeshkina, N. A., Bulygin, K. N., Graifer, D. M., Meshchaninova, M. I., Repkova, M. N., Ven'yaminova, A. G., Karpova, G. G.
• Format: Article
• Language: English
• Subjects: Bacteria
• ISSN: 0026-8933; 1608-3245
• DOI: 10.1023/B:MBIL.0000008355.58743.93

Oligoribonucleotide derivatives containing Phe codon UUC along with a 3'-flanking sense or stop codon with a perfluoroarylazido group at G or U were used to study the positioning of each nucleotide of the latter codon relative to the 18S rRNA in the A site of the 80S ribosome. To place the modified sense or stop codon in the A site, tRNA^sup Phe^ cognate to UCC was bound in the P site. Regardless of the position in the sense or stop codon, the modified nucleotide crosslinked with invariant dinucleotide A1823/A1824 and nucleotide A1825 in helix 44 close to the 3' end of the 18S rRNA. Located in the second or third position of either codon, the modified G bound with invariant nucleotide G626, which is in the evolutionarily conserved 530 stem-loop fragment. The results were collated with the X-ray structure of the bacterial ribosome, and the template codon was assumed to be similarly arranged relative to the small-subunit rRNA in the ribosomal A site of various organisms.[PUBLICATION ABSTRACT]